The use of genomic data to enable discovery of novel biological processes, often referred to as genome mining, has the potential to revolutionize numerous areas of modern biology. Among these, the field of natural product discovery lies near the top. These biologically-produced small molecules have been the source or inspiration for nearly two-thirds of all human medicines (Reference 1), yet research in this area has dwindled in recent years due to high costs and increasing rates of rediscovery. Within the natural product biosynthesis field, it has been widely suggested that the solution to these problems lies in the use of genome mining (References 2,3). Thus, by focusing research efforts on strains that encode natural product biosynthetic genes with uncharacterized products, one can de-replicate, streamline and accelerate the discovery process. Indeed, genome mining has led to the discovery of several novel natural products (References 2-4). While these successes clearly demonstrate the feasibility of the approach, the studies conducted to date have been limited to individual strains or small collections. If we hope to revitalize the use of natural products in the pharmaceutical industry, genome mining must be realized as a high-throughput discovery process superior to currently used methods. Here, we show the feasibility of this approach in a campaign to identify the full repertoire of phosphonic acid natural products produced by collection of over 10,000 actinobacteria. 
Phosphonic acid natural products possess a number of traits that make them ideal candidates for large-scale genome mining. First and foremost, phosphonates have great pharmaceutical potential, with a commercialization rate of 15% (3 of 20 isolated compounds) (Reference 5), much higher than the 0.1% average estimated for natural products as a whole (Referenece 6). The potent bioactivity of phosphonates derives from their chemical mimicry of essential metabolites, including phosphate esters and anhydrides, as well as carboxylate reaction intermediates (Reference 5). Given the ubiquitous presence of these chemical moieties in biology, phosphonates are unrivaled in the range of targets they can potentially affect. Consistent with this idea, phosphonates with herbicidal, insecticidal, antibacterial, antiparasitic, antiviral and antihypertensive activities are known. Notable examples include fosfomycin (Monurol®), clinically prescribed for acute cystitis, FR-900098 and fosmidomycin, antimicrobials undergoing clinical trials for malaria, and phosphinothricin, the active component in several commercial herbicides (Liberty®, Basta®, and Rely®). (References 5, 7). Second, the methodology needed for gene-based discovery of phosphonate biosynthetic loci has already been established). This method relies on the fact that all but two characterized phosphonate biosynthetic pathways begin with the enzyme phosphoenolpyruvate mutase, encoded by the pepM gene. Thus, amplification of an internal fragment of the pepM gene with degenerate PCR primers allows identification of strains or plasmid clones that encode phosphonate biosynthetic pathways. Third, gene-based surveys have proven that phosphonate biosynthesis is relatively common in microorganisms, with the greatest diversity of unexplored biosynthetic pathways observed within Actinobacteria (Reference 13). Finally, the unique chemical properties of the carbon-phosphorus bond allow direct and unambiguous identification of phosphonates in complex mixtures of metabolites using mass-spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy, even when the structure of the molecule in question is unknown (References 14, 15). These detection methods facilitate the purification and characterization of phosphonate natural products, a process that is, at best, extremely laborious for other natural product classes that lack analogous class-specific analytical chemistry assays.
The discovery of natural products, an important source of human medicines, is critical for the development of new therapeutics against health threats including cancer and multi-drug resistant pathogens. Yet in recent years, industrial development of pharmaceuticals from natural products has been stymied due to a variety of reasons, including the repeated discovery of previously known compounds. Here we demonstrate large scale genomics as one potential solution to this problem by mining a collection of 10,000 actinomycetes for novel phosphonic acids, an important class of natural products with antimicrobial, -viral, -malarial, and herbicidal activities. The framework described here provides a foundation for rapid, large-scale discovery of other classes of natural products and their use as lead compounds in the pharmaceutical industry.